Fix bug when creating JSON output for merges.

Fixed bug when creating the JSON for merged segments where more than
one file was produced. Instead of then splitting segments into different
entries in the outer array of the JSON, the segments have been written
to the inner array instead.

apps/seg/Testing/CMakeLists.txt

@@ -50,6 +50,7 @@ dcmqi_add_test(
       --outputDICOM ${MODULE_TEMP_DIR}/liver_heart_seg_reordered.dcm
     )
 
+
 find_program(DCIODVFY_EXECUTABLE dciodvfy)
 
 if(EXISTS ${DCIODVFY_EXECUTABLE})
@@ -139,6 +140,22 @@ dcmqi_add_test(
       ${itk2dcm}_makeSEG_multiple_segment_files_reordered
     )
 
+    dcmqi_add_test(
+      NAME ${dcm2itk}_makeNRRD_merged_segment_file
+      MODULE_NAME ${MODULE_NAME}
+      COMMAND ${SEM_LAUNCH_COMMAND} $<TARGET_FILE:${dcm2itk}Test>
+        --compare ${BASELINE}/liver_seg.nrrd ${MODULE_TEMP_DIR}/makeNRRD_multiple_segments-1.nrrd
+        --compare ${BASELINE}/spine_seg.nrrd ${MODULE_TEMP_DIR}/makeNRRD_multiple_segments-2.nrrd
+        --compare ${BASELINE}/heart_seg.nrrd ${MODULE_TEMP_DIR}/makeNRRD_multiple_segments-3.nrrd
+        ${dcm2itk}Test
+        --inputDICOM ${MODULE_TEMP_DIR}/liver_heart_seg.dcm
+        --outputDirectory ${MODULE_TEMP_DIR}
+        --prefix makeNRRD_merged_segment_file
+        --mergeSegments
+      TEST_DEPENDS
+        ${itk2dcm}_makeSEG_multiple_segment_files
+      )
+
 dcmqi_add_test(
   NAME seg_meta_roundtrip
   MODULE_NAME ${MODULE_NAME}
@@ -160,8 +177,6 @@ dcmqi_add_test(
     ${dcm2itk}_makeNRRD_multiple_segment_files
   )
 
-
-
 set(TEST_SEG_SIZES 24x38x3 23x38x3)
 
 foreach(seg_size ${TEST_SEG_SIZES})

include/dcmqi/JSONSegmentationMetaInformationHandler.h

@@ -38,7 +38,7 @@ namespace dcmqi {
     // segGroupNumber starts with 0 and refers to the item in segmentsAttributesMappingList.
     // if segGroupNumber is invalid, create segment within a newly created segmentation group
     // otherwise add segment to the existing segmentation group identified by segGroupNumber
-    SegmentAttributes* createOrGetSegment(const int segGroupNumber, unsigned labelID);
+    SegmentAttributes* createOrGetSegment(const unsigned int segGroupNumber, unsigned labelID);
 
   protected:
 

libsrc/JSONSegmentationMetaInformationHandler.cpp

@@ -151,25 +151,21 @@ namespace dcmqi {
     return values;
   }
 
-  SegmentAttributes *JSONSegmentationMetaInformationHandler::createOrGetSegment(const int segGroupNumber, const unsigned labelID) {
-    //std::cout << "DEBUG: num segmentations: " << this->segmentsAttributesMappingList.size() << std::endl;
-    /*
-    for (vector<map<unsigned,SegmentAttributes*> >::const_iterator vIt = this->segmentsAttributesMappingList.begin();
-       vIt != this->segmentsAttributesMappingList.end(); ++vIt) {
-      for(map<unsigned,SegmentAttributes*>::const_iterator mIt = vIt->begin();mIt!=vIt->end();++mIt){
-        SegmentAttributes *segmentAttributes = mIt->second;
-        if (segmentAttributes->getLabelID() == labelID)
-          return NULL;
-      }
-    }*/
+  SegmentAttributes *JSONSegmentationMetaInformationHandler::createOrGetSegment(const unsigned int segGroupNumber, const unsigned labelID) {
+    if (segGroupNumber < 1)
+    {
+      std::cerr << "ERROR: Segment group number must be >= 1" << std::endl;
+      return NULL;
+    }
 
     SegmentAttributes *segment = new SegmentAttributes(labelID);
-    if (this->segmentsAttributesMappingList.size() < segGroupNumber+1) {
+    if (this->segmentsAttributesMappingList.size() < segGroupNumber) {
       map<unsigned,SegmentAttributes*> tempMap;
       tempMap[labelID] = segment;
       this->segmentsAttributesMappingList.push_back(tempMap);
-    } else
-      this->segmentsAttributesMappingList[segGroupNumber][labelID] = segment;
+    } else {
+      this->segmentsAttributesMappingList[segGroupNumber-1][labelID] = segment;
+    }
 
     return segment;
   }

libsrc/OverlapUtil.cpp

@@ -324,7 +324,6 @@ OFCondition OverlapUtil::getSegmentsByPosition(SegmentsByPosition& result)
         DCMSEG_DEBUG(ss.str());
     }
     DCMSEG_DEBUG("groupFramesByPosition(): Grouping segments by position took " << tm.getDiff() << " s");
-
     return cond;
 }